Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling

Abstract

BackgroundSorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having differential response to low-N stress.ResultsIllumina RNA-sequencing detected several common differentially expressed genes (DEGs) between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk). In sensitive genotypes, N-stress increased the abundance of DEG transcripts associated with stress responses including oxidative stress and stimuli were abundant. The tolerant genotypes adapt to N deficiency by producing greater root mass for efficient uptake of nutrients. In tolerant genotypes, higher abundance of transcripts related to high affinity nitrate transporters (NRT2.2, NRT2.3, NRT2.5, and NRT2.6) and lysine histidine transporter 1 (LHT1), may suggest an improved uptake efficiency of inorganic and organic forms of nitrogen. Higher abundance of SEC14 cytosolic factor family protein transcript in tolerant genotypes could lead to increased membrane stability and tolerance to N-stress.ConclusionsComparison of transcriptomes between N-stress tolerant and sensitive genotypes revealed several common DEG transcripts. Some of these DEGs were evaluated further by comparing the transcriptomes of genotypes grown under full N. The DEG transcripts showed higher expression in tolerant genotypes could be used for transgenic over-expression in sensitive genotypes of sorghum and related crops for increased tolerance to N-stress, which results in increased nitrogen use efficiency for sustainable agriculture.

Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

“…The high-affinity nitrate transporter gene families (NRT2 and NRT3) co-function as a tetramer containing two subunits of each (Yong et al, 2010) and play a critical role in nitrate uptake as they are upregulated in roots during limited N conditions in sorghum (Gelli et al, 2014). An ancient whole-genome duplication in sorghum (Paterson et al, 2004) resulted in the formation of sub-functional protein complexes, and there are examples of asymmetrical evolutionary rates between such subunits (e.g., ADP-glucose pyrophosphorylase; Georgelis et al, 2008; Corbi et al, 2011).…”

“…Only those genes found to be expressed were used for analysis in this study, irrespective of expression levels. Of note, this database also includes expression data from sorghum exposed to N-stress, highlighting upregulation of genes involved in N stress response, however this analysis was limited to roots (Gelli et al, 2014). A total of 230 expressed genes were identified for potential involvement in the N biosynthetic pathway.…”

Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis

“…Improving biomass production will require maximizing yield while reducing costly inputs, including nitrogen (N), and water (Fazio & Monti, , National Research Council, ). Fortunately, sorghum possesses significant genetic diversity for N use efficiency (Gelli et al., , ), yield potential and drought tolerance (Mace et al., ). Furthermore, the availability of a reference genome (Paterson et al., ), an expression atlas (Shakoor et al., ), and over 400,000 markers (Morris et al., ) identified for marker‐assisted breeding makes sorghum well‐suited for significant crop improvement.…”

Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum

“…Differential expression of gene transcripts between parents and RIL bulks were calculated from the transcriptomes (RNA-seq data) generated earlier [65] on the root tissues of different sorghum genotypes grown under N-stress. False discovery rate (FDR) ≤ 0.001 and the absolute value of |log 2 (Fold change) | ≥ 1 were used as thresholds to judge the significance of differences in transcript abundance.…”